Doctor Whooves Episode 6: A Ponyville Invasion
by The 1597 Faceless Writer
Summary: The Doctor finally manages to return Twilight to 1002, only to discover that he's brought her back a little bit late. As the suspicious citizens of Ponyville turn on the Doctor, a strange army led by an old foe invades the town.
1. Prologue

Author's Note: I now present the sixth episode in the tale of Doctor Whooves. Enjoy!

Doctor Whooves: Episode 6

A Ponyville Invasion

Prologue

_**Home of Twilight Sparkle, Ponyville, Equestria, Gaia, Autumn, 1002 C.E.**_

Twilight sighed as the TARDIS came to another bumpy stop. This was it. She was home. She knew it.

"There we go!" exclaimed the Doctor. "Outside those doors lies Ponyville, 1002 C.E."

"Home," said Twilight with a smile. The Doctor smiled too as he walked towards the doors. He opened them and beckoned Twilight outside. She slowly approached the doors and walked through them.

The familiar scent of books reached her nose as she stepped out of the TARDIS. There it was. Her library. Her home. Nothing had changed. A huge smile appeared on her face as she began running alongside the outline of the library, carefully examining each book.

"Everything's in place! Nothing's changed at all! How...how long were we gone?" she asked.

"About five minutes," the Doctor replied.

"Five minutes? All that happened in a mere five minutes?"

"That's one of the perks of having a time machine."

"Spike and the others must be worrying about me. I better go let them know that I'm okay!"

"You go and see your friends. I think I'll go take a quick walk around town."

"Okay!"

Twilight ran up to the Doctor and hugged him tightly.

"Thank you for bringing me home!" she said. The Doctor hugged her back and nodded his head.

"I promised I would, didn't I?" he replied. Twilight gave the Doctor and quick kiss on the cheek before running through the front door. The Doctor smiled and followed suit. He looked and watched as Twilight disappeared around a bend. As he closed the door behind him, he noticed something taped to the exterior of the door. It was a piece of paper with a picture of Twilight printed on it. As he examined the paper, his eyes grew incredibly wide. "Oh no! Not again!"

_**Outside Town Hall, Ponyville, Equestria, Gaia, Autumn, 1002 C.E.**_

It didn't take long for Twilight to realize that something was wrong. The air was colder than it should have been and nopony was out and about. Twilight soon began to notice brown leaves scattered on the ground. Something was wrong. Something was horribly wrong. She could hear talking emanating from within Town Hall.

"I guess a town meeting is going on," she said out loud. "Wait a minute. How could the entire town crowd into Town Hall in under five minutes? That's quite impossible. Unless-"

The talking stopped and the doors leading into Town Hall flung open. Ponies began filing out through the doors. They, however, all came to a halt when they saw Twilight. Their eyes grew large and their jaws dropped.

"Uh...hey, everypony. Did I miss the town meeting? I'm sorry. Don't worry though! The creature has been taken care of!" Twilight announced awkwardly, assuming that the meeting had something to do with the Dalek attack. Suddenly, a familiar purple and green dragon emerged from the crowd.

"Twilight?" asked Spike. He looked as shocked as the other ponies.

"Yes, Spike? Is there a problem?"

Tears formed in Spike's eyes as he lunged towards her and wrapped her in a giant hug. Five familiar mares broke free from the crowd and also hugged Twilight.

"You're back!" cried Pinkie Pie.

"Where in tarnation have you been?" Applejack asked.

"We have simply been _dying_ with worry about where you could have possibly gone!" cried Rarity.

"What the hay happened to you?" Rainbow Dash snapped.

"We were so worried!" exclaimed Fluttershy. Twilight broke free from their grasp and slowly backed up.

"What's going on?" she asked. "According to the Doctor, I've only been gone five minutes."

The five mares and Spike looked at each other nervously and then turned back to Twilight. They looked just as confused, if not more confused, than she did. Applejack took a step forward.

"Twilight...ah don't know how to say this, but you haven't been gone five minutes. You've been missing for five _months_!" she exclaimed.


	2. Prime Suspect

Chapter 1: Prime Suspect

_**Outside Town Hall, Ponyville, Equestria, Gaia, Autumn, 1002 C.E.**_

The gravity of Applejack's words hit Twilight like a brick. She felt as though she was about to upchuck her entire stomach. She'd been missing for five months! While she was off traveling with the Doctor, fighting strange enemies, and helping ponies throughout time and space her friends were worrying and looking for her for five whole months!

"It can't be," Twilight choked.

"It's true!" said Pinkie Pie. "I remember the day exactly! It was June 19. That was exactly five months ago!"

"That's when the metal thingy attacked the town and that strange stallion showed up!" said Rainbow Dash.

"Don't worry, Twilight! We'll make sure _he_ doesn't get away with whatever he did to you!" Spike said. His face was full of rage and Twilight could see five months of sadness hiding away behind those eyes. Then she realized what was happening. Everypony thought that the Doctor had kidnapped her!

"Wait!" she said. "It's not what it looks like! You see-"

"Twilight!" called a familiar voice. Twilight groaned as she looked back to see the Doctor running towards her. "We've arrived a tad bit late!"

"A tad?! You call five months a _tad bit late_?!"

"Well-"

"There he is!" Rainbow Dash snapped. "There's the pony that kidnapped Twilight!"

"What?"

"Get him!" cried the crowd.

"WHAT?!"

"WAIT!" Twilight cried. But her cries proved fruitless as the crowd of ponies charged at the Doctor. The Doctor turned and ran like he had never run before.

The Doctor could hear the ponies screaming behind him. He didn't dare look back. He knew that would lead to him getting caught and kicked into a pulp. He made a quick turn and ran for the library. The TARDIS was his last safe haven. Normally he would try to talk sense into them but it's hard to talk sense to a wall of ponies, pegasi, and unicorns charging at you with the full force of their bodies. The pegasus known as Rainbow Dash was certainly giving him the shivers. He remembered meeting her in Sugar Cube Corner when the Dalek had appeared. Even though he had known her for a couple minutes at max, he knew that she was not a pony that you wanted to tick off. Sadly, he had managed to tick her off by making her friend disappear off the face of the planet for five months. Obviously, that was a big mistake.

"Come back here!" snapped Rainbow Dash as she flew towards the Doctor. The Doctor dodged her barrel roll and made his way down a nearby street. He turned back just in time to feel a pair of hooves grab him and pull him into a nearby alleyway. A hoof covered his mouth and he watched as the crowd of ponies rushed past the alleyway entrance. "Where the hay did he go off to?!"

It wasn't until the sound of the crowd had disappeared that the hoof wrapped around the Doctor's mouth moved aside. The Doctor turned to find himself staring into a pair of bright, yellow eyes. The eyes randomly pointed off in awkward directions for a few seconds before returning to a normal state. It wasn't until the Doctor saw the gray coat, the wings, and the blonde mane that he realized who had saved him.

"You've got a lot of explaining to do, Mr. Doctor!" snapped Derpy Hooves.

_**Home of Twilight Sparkle, Ponyville, Equestria, Gaia, Autumn, 1002 C.E.**_

This was a disaster. Plain and simple. Not only had she returned five months late but now the Doctor, the stallion who saved Ponyville as well as many other places throughout time and space, was now being accused of kidnapping her. She opened the door and trudged inside the library. Owlowiscious flew down from upstairs and hooted with delight at the return of his owner.

"Hi, Owlowiscious," she sighed. She looked around the library and noticed just how cleaned up it was. It was surprisingly clean for a library that hadn't been organized regularly in five months. "It's certainly clean in here."

"You can thank Spike for that," said a small voice. Twilight turned to see Fluttershy standing in the doorway.

"Fluttershy. I thought you went with the others."

"I don't like mobs. They frighten me."

"No surprise there. Listen, Fluttershy. You've got to help me tell the others that this is just one huge misunderstanding! The Doctor did not kidnap me!"

Fluttershy fell silent. Twilight noticed that she was staring at the TARDIS, which was still parked in the middle of the library.

"Spike told me about that blue box. Is it true that it's his ship?" she asked. Twilight nodded as Fluttershy approached the TARDIS. "What happened, Twilight? Where did you go?"

"Do you remember what happened five months ago? The Dalek attack?" Twilight asked.

"What's a Dalek?"

"It's the creature that attacked Ponyville the day I went away with the Doctor."

"I never saw it. I was home alone all day with Angel."

"The Doctor and I defeated it. The Dalek, however, damaged the ship and it took us away."

"To where?"

"Other places in space...and time."

"Are you saying that you-"

"Traveled through time? Yes. That's exactly what I'm saying. We traveled 1000 years in the future, we visited a fort on another planet in 1899, we traveled to Canterlot in 987, and our last stop was Equestria 100 years prior to Princess Celestia's birth."

"That's...unbelievable."

"Tell me about it. So...Spike told you about the TARDIS?"

"That's what it's called? Well, yes. Spike and Princess Luna told us all about the Doctor and his mysterious arrival. From what we gathered, I guess it was only natural for us to assume that he had kidnapped you...or something worse had happened."

Twilight sighed. She thought about the last time she had seen Spike before heading off with the Doctor.

"I promise I'll come back! Don't I always keep my promises?" she had said. For her, it had been around a few days at max since that occurred. For Spike, it had been five months, nearly half a year. The thought made Twilight sick to her stomach. Twilight looked at Fluttershy and said, "Come on. I need you to help me calm down the others."

Fluttershy nodded and Owlowiscious flew back up to his perch. Twilight and Fluttershy then exited the library.

_**Home of Derpy Hooves, Ponyville, Equestria, Gaia, Autumn, 1002 C.E.**_

The Doctor sat awkwardly across from the gray pegasus. The hunting party had grown quiet and the Doctor was happy for that. He eagerly scarfed down the blueberry muffin that Derpy had given him as a snack.

"Thank you for the snack, and saving my rump back there. I really owe you one, Ms. Hooves," he said.

"Just call me Derpy, Mr. Doctor. That's what everypony else calls me," she replied.

"Only if you drop the _Mr._ bit. I prefer to just be called Doctor, thank you very much."

"Okay then!"

Derpy giggled as the Doctor took one last bite from his muffin. Once the muffin was gone, Derpy instantly began staring the Doctor down.

"Now let's cut to the chase! Did you or did you not kidnap Twilight Sparkle?" she asked.

"I did not kidnap her. Me taking her away was a complete accident. That damn Dalek is to blame. Screwing up my controls and damaging my TARDIS. Isn't that just inconsiderate?!" the Doctor replied.

"I guess."

"Do you believe me?"

"Actually, I do."

"That's good."

"Question. Do you happen to know a mare with a dark red coat, a purple mane, and blue eyes?"

"I actually do. Her name's Matilda."

"You can thank her for me believing you. She appeared to me on the day Twilight disappeared."

"Did she say anything?"

"She said that she knew me well and that I had an adventurous future waiting for me. I think it had something to do with you and Twilight."

"Tell me, Derpy. Do you know Twilight Sparkle and her friends well?"

"Not really. I'm just one of those background ponies. I don't talk to or know a lot of other ponies."

"This town seems pretty upset about Twilight disappearing."

"Well Twilight represents one of the Elements of Harmony and she's a pupil of Princess Celestia herself. She's a very well-known pony around town. Her disappearance has probably affected Princess Luna the most."

"How so?"

"When Princess Celestia came to Ponyville to learn about the details regarding Twilight's disappearance, Luna was the one to fill her in. She told Celestia about her interactions with you and Celestia didn't take kindly to that."

"What do you mean by that?"

"Celestia told Luna that she was foolish to leave Twilight, her star pupil, unprotected and allow her to get kidnapped by a _strange stallion_. Luna's had it rough the past five months."

"Well I plan on mending things as soon as possible. Once I manage to clear everything up."

"I hardly doubt a lot of the ponies in this town are going to listen to you, no offense. Rainbow Dash is going to be especially hard to move."

"No offense taken and I see what you mean. I just need to find Twilight and then we can establish a game plan."

"Okay. But we've got to be careful. Until we get things straightened out, you're public enemy #1."

"Got it."

The Doctor and Derpy made their way through the front door and out into the cold autumn air.

_**Zecora's House, Everfree Forest, Equestria, Gaia, Autumn, 1002 C.E.**_

Zecora the zebra was preparing a new batch of potions in her house when she heard a peculiar sound emanate from outside. She walked towards the door and poked her head out.

"Who is there, if I may ask? Perhaps a pony with another task?" she asked. The sounds stopped but a small light appeared off in the distance. Zecora instantly recognized the light as that of a fire and began making her way towards the source. "Careful, friend, that is not good, for a flame is no ally to wood!"

Zecora was so focused on reaching the source of the fire that she didn't notice the two, tall, dark figures approach her from behind. There was a swinging motion, Zecora felt a sharp pain rush through her skull, and she blacked out.


	3. The Doll

Chapter 2: The Doll

_**Sugar Cube Corner, Ponyville, Equestria, Gaia, Autumn, 1002 C.E.**_

The Doctor and Derpy quietly entered the pastry shop and were happy to find that it was empty at the current moment. They could hear snoring coming from the upstairs rooms and decided to try and be as quiet as possible.

"Why would Twilight come here?" the Doctor asked.

"I've seen her and her friends hang out here often. I'm sure that she'll turn up eventually," Derpy replied.

"So who's upstairs?"

"It must be the Cakes. They've been really busy of late."

"The Cakes? I think I met Mrs. Cake when I first came here."

Suddenly, they heard footsteps from upstairs.

"Is anypony else here by any chance?" the Doctor asked.

"Well the Cakes have twin foals but they're also asleep. Pinkie Pie lives here but, last time I checked, she was off with the others," Derpy said as both she and the Doctor turned towards the ceiling.

"So if the Cakes and their children are asleep and Pinkie Pie's out, then who's moving about upstairs?"

Derpy gulped. The Doctor began making his way towards the stairs. Derpy jumped in front of him and snapped, "What are you doing?! You can't just go up into somepony's home!"

"I think it's safe to assume that somepony, aside from us, has broken into this shop and they probably have less innocent intentions than we do."

"Do you think it's safe?"

"No. We could be dealing with a thief or a killer. Of course it isn't safe. But, think about it this way, the Cakes are in the same amount of danger as we are, maybe even more. We need to help them if somepony else really has broken into the shop."

"I guess you're right. You won't let anything bad happen to them...or me will you, Doctor?"

"Of course not! Come on then!"

The Doctor and Derpy snuck up the stairs and tried to make as little of a ruckus as possible. The Doctor learned all too quickly that Derpy had a talent for clumsiness as she nearly knocked over a vase and smacked him in the face with one of her wings. He assumed this had something to do with her eyes that became inverted every few minutes. He wanted to ask her about it but something told him that would not be a wise decision. The footsteps grew louder with every passing second as they came closer to the top of the stairs. A long hallway greeted them at the top of the stairs. There was nopony in sight and the footsteps, unfortunately, had died down. Fortunately, the Doctor remembered which direction the footsteps were coming from. He and Derpy took baby steps as they edged their way towards the source of the footsteps. Soon they were standing in front of the bedroom door of Pound Cake and Pumpkin Cake. The Doctor nodded at Derpy and slowly pushed the door open.

The footsteps stopped as they entered the room. A glowing nightlight hung from the ceiling and the twins slept soundly in their cribs. There was nopony else in the room.

"I could have sworn that the footsteps were coming from in here," said the Doctor as he entered the room. He pulled out his Sonic Screwdriver and began examining the dark room from top to bottom. Derpy stood close to him.

"Doctor," she said.

"Just a minute."

"_Doctor_."

"Just give me a second!"

"_Doctor!_"

"What is it?!"

"I think I hear somepony else breathing."

The Doctor listened carefully. He could hear his own breathing, he could hear Derpy's breathing, he could hear the twins' breathing, and he could hear somepony else breathing. It was a raspy, cold sound that sent shivers down the Doctor's spine. He quickly realized that the breathing was coming from behind him and Derpy.

"Don't move!" he whispered into Derpy's ear. Derpy gave a slight nod and gulped. A cold bead of sweat trickled down the Doctor's face as the foreign breathing grew louder and louder. The Doctor aimed his Sonic Screwdriver and turned around. That's when the door to the bedroom slammed shut and the nightlight turned off, leaving them in complete darkness.

_**Town Hall, Ponyville, Equestria, Gaia, Autumn, 1002 C.E.**_

Twilight and Fluttershy entered Town Hall to see Spike, Applejack, Rainbow Dash, Pinkie Pie, Rarity, and a few other ponies talking amongst each other.

"Twilight!" said Spike as he approached them. "Where did you run off to?!"

"I went back to the library for something. Listen, Spike. This is all a huge misunderstanding!" Twilight replied.

"What do you mean?"

"The Doctor didn't kidnap me. It was a complete accident that I went away with him."

"Are you sure? How do we know that he didn't alter your memory?" asked Rainbow Dash.

"Really? Are you really going down that road? The Doctor did nothing to my memory. The Doctor saved Ponyville from the creature that attacked the town back in June! The Doctor's guilty of nothing but helping us out!"

"Then why did he run away when we accused him?!" Rarity asked.

"Maybe it's because he saw a wall of ponies charging towards him and he thought that he should get out of there before he was trampled to death."

Twilight raised one of her eyebrows and the others fell silent.

"If Twilight trusts him, then I do too," said Fluttershy. Twilight looked at Spike. She could tell that he was holding back some anger.

"I don't know. I'm still a little bit sketchy about this _Doctor_," said Rainbow Dash. "What's his real name anyway?"

"I don't know. That's just what he goes by. He's just the Doctor," Twilight replied. "I think it would be easier to find him if everypony stopped hunting him like he was a wild animal. Call off the hunt and I'll bring him here to clear things up for you."

"Sounds good," said Applejack.

"Okie-dokie-lokie!" Pinkie Pie exclaimed.

"Fine," Spike grumbled. Twilight wanted to ask the dragon what was wrong but she figured that she would save that for a more private moment.

"So where do we start looking?" Rainbow Dash asked.

"He wasn't at the library and the TARDIS, his ship, is still there so I can assume that he hasn't returned there yet," said Twilight.

"Why don't we start with Sugar Cube Corner?" Pinkie Pie suggested.

"Why there of all places?"

"I dunno! I've just got a feeling that that's where we need to be!"

"Is it your Pinkie Sense again?"

"Nope! It's just...a feeling."

"Okay then. I guess that's a good place to start if any."

Twilight then turned around and led the five mares and the dragon out through the front doors.

_**Sugar Cube Corner, Ponyville, Equestria, Gaia, Autumn, 1002 C.E.**_

The Doctor activated the Sonic Screwdriver, which proceeded to emit a glowing ball of blue light which floated towards the ceiling, illuminating the room.

"That's new!" exclaimed the Doctor as he turned towards the door. What he saw was definitely not what he expected. At first glance, it looked like a pony. But further inspection revealed an even more disturbing adversary. It looked like a pony but its coat consisted of random pieces of fabric and cloths sewn together. It had a mane made up of broom bristles, rope, ribbons, and pieces of fake hair. It had a zipper for lips and the zipper was open at the moment, allowing the jaw to droop like a wet flower. It had a tongue made up of plastic and had sharp teeth made out of razor blades. It was around the height of an average mare and it had two black buttons for eyes. The Doctor could only think of a life-sized voodoo doll when he saw the creature. The giant doll turned towards the Doctor and Derpy and let out a wheezy sound that resembled that of a laugh. The doll's mane began to expand and grow, each lock of fake hair acting like a tentacle wishing to ensnare its prey. The doll stood on its hind legs and its belly opened up like a backpack, revealing a dark cavity big enough to hold two ponies. The tentacles then flew for them. "Dodge!"

Derpy took to the air and the Doctor jumped, each just barely managed to dodge the attacking mane. The hair continued to grow and stretch as it tried to capture them. The Doctor used the Sonic Screwdriver to confuse one of the locks into attacking another arm of hair. He was trying to figure out the new abilities that his Sonic Screwdriver now had due to its arrival in Equestria but he decided to save that for later. Derpy yelped as one of the arms grabbed her leg. More arms wrapped around her body and began pulling her towards the doll.

"Doctor!" she cried as the black cavity grew closer and closer. The Doctor charged at the doll, dodging its living hair in the process, and kicked it with his two front legs. The doll stumbled for a bit but let go of Derpy. "Look out!"

The Doctor felt a group of arms wrap around him and throw him into the black cavity. He tried to escape but the fabric inside of the doll bound him in place. It was then that he realized that he had dropped his Sonic Screwdriver outside of the doll.

"Derpy! Get my Sonic Screwdriver!" he called. Derpy saw the Doctor's Screwdriver lying on the floor a few feet away from her. She reached for it and pointed it at the doll.

"What do I do with it?!" she asked. The arms began reaching for her once again.

"Just click the button and pray that something helpful happens!"

Derpy clicked the button and several of the arms became lifeless. Some of the arms even began attacking each other.

From inside the doll, the Doctor heard a familiar voice say, "Enough! You've got the Doctor! Leave his helper and bring him to me!"

The opening in the doll's belly sealed up and the arms retracted, leaving the Doctor in complete darkness. The doll then raced out of the room and towards the stairs. Derpy flew after it.

"I wish I were Rainbow Dash!" she groaned as she chased the doll down the stairs. The Doctor felt like a sock inside of a washing machine. Riding inside of a living doll was far from the most comfortable form of transportation.

"The TARDIS is smoother than this!" the Doctor groaned as the doll jumped the last couple steps. Suddenly, a series of voices rang out from outside the doll.

"Doctor?! Are you here?" called the voice of Twilight Sparkle. Suddenly, the doll came to a halt. Derpy rounded a bend to find the doll in the center of the shop. Twilight, Spike, Applejack, Rainbow Dash, Pinkie Pie, Fluttershy, and Rarity stood in its way.

"What in tarnation is that?!" exclaimed Applejack.

"Is that a doll?" Rarity asked. The doll growled and Derpy knew that it was about to extend its arms again.

"It's got the Doctor!" Derpy cried. "Be careful! It's dangerous!"

Twilight barely had a second to react as the doll's hair arms flew towards her. The mares scattered. Spike shot a blast of green fire at one of the arms. The doll screamed in agony as one of its arms burned.

"Nice job, Spike!" exclaimed Rarity.

"Thanks! I've been working on that!" Spike boasted.

"Save it for later, guys!" said Rainbow Dash as she pushed them out of the way of another set of arms. Derpy used the Sonic Screwdriver to confuse another set of arms and Twilight shot a magical fireball at the center of the doll. The Doctor felt the fibers around his legs loosening.

"No!" cried the voice from inside the doll. "Bring the Doctor to me! Bring the Doctor and Twilight Sparkle to _me_!"

The pony doll whinnied like a horse from Earth and charged for Twilight along with its arms. Pinkie Pie jumped over the counter. She had a kitchen knife in her mouth.

"Watch out, Twilight!" she warned as she stabbed the knife into the doll's belly. The Doctor's eyes widened as the blade stopped a few inches from his face. Pinkie brought the knife down, cutting a massive hole in the doll's stomach. The Doctor pulled himself out of the doll and Pinkie helped pull him away from the flailing arms. Twilight shot a fireball into the doll's belly and Spike followed suit with a blast of green fire. The doll screamed as its body began to burn with a mix of orange and green flames. Within seconds, the doll and its arms were nothing but scorched ashes on the shop floor. The Doctor, Twilight, Derpy, and the others were all breathing heavily.

"That was fun," said the Doctor sarcastically.

"I don't think it was," Pinkie replied.

"What the hell was that?!" Rainbow Dash snapped as she flew at the Doctor, coming to a halt a few inches from his face.

"Using the word _hell_ instead of _hay_ now, I see."

"I only do that when I'm _really_ peeved!"

"I'm guessing that this is one of those moments."

"You got it!"

"Listen, I'm just as confused as you are, Ms. Dash."

"Please don't call me _Ms. Dash_. Rainbow Dash will do just fine."

"Was that a _living_ doll, Doctor?" Derpy asked.

"Looks that way," the Doctor replied.

"I've seen many strange things but ah have to admit that that was definitely one of the top ten," said Applejack.

"I wonder what it wanted," said Fluttershy.

"What _it _wanted isn't what matters. What its _master_ wanted is what matters," said the Doctor.

"It's master?" Twilight asked.

"While I was inside it, I heard a voice calling out orders to it. From what I can gather, the doll's master wants you and me. And she wants us _very_ badly."

"So it was a she?"

"Yes. The voice sounded oddly familiar though. It was almost as if I've heard it somewhere before."

"We should look into this."

"Right!"

"Now wait just a minute!" Spike snapped. The Doctor, Twilight, and the others looked down at the dragon. "I want to know what exactly happened to Twilight five months ago!"

"Spike," Twilight sighed. She tried to calm him down but it was no use. Spike approached the Doctor and pointed one of his claws towards the Doctor's face.

"Five months ago, _you_ show up out of the clear blue with your strange box. You mutter a bunch of random stuff to me, Twilight, and Princess Luna right before some creature attacks our town looking for you! Twilight runs off to help you and you, her, and your box disappear off the face of the planet! For five months, I was worried about whether or not Twilight was still alive! Princess Luna had to pay consequences for having Twilight disappear under her watch! Then, after five long months, you just randomly show up out of the blue and bring more monsters to our town! I want an explanation now!"

"Spike, it isn't his fault!"

"Even if he isn't completely at fault here, I still want to know what happened! I want to know why that creature attacked us! I want to know where you two went off to for five months! I want to know...why you left with him, Twilight."

Twilight fell silent. That familiar, sickening feeling was bubbling up in her stomach again. Her eyes began watering up. She knelt down to Spike's level and hugged him. Tears were beginning to roll down his and her cheeks.

"I'm so sorry, Spike! I'm sorry that I disappeared for five months! I didn't mean to! It was just a huge accident!" she cried.

"What happened to you, Twilight?" he asked.

"After I left Sugar Cube Corner, I chased after the Doctor and the creature, which is called a Dalek by the way. I teleported to the library and helped the Doctor inside. The Doctor and I then led the Dalek into the TARDIS, his ship, and defeated it. However, the Dalek had damaged the ship and the ship automatically took us away."

"Where did you go?"

"The Doctor and I-"

Suddenly, a series of screams began emanating from outside. They looked out through the windows of the shop to see ponies running through the streets.

"What's going on?" asked Derpy. The Cakes walked down the stairs and approached the group. Pound Cake and Pumpkin Cake were just now waking up.

"What's all the ruckus about?" asked Mrs. Cake. Her eyes then fell upon Twilight. "Twilight! You're back!" She then turned to the Doctor. "It's _you_."

"We better find out what all the fuss is about," said Applejack.

"I have a bad feeling about this," said Rarity.

"I think we all do," said Twilight.


	4. An Abnormal Army

Chapter 3: An Abnormal Army

_**Outside Sugar Cube Corner, Ponyville, Equestria, Gaia, Autumn, 1002 C.E.**_

The Doctor, Twilight, Derpy, Spike, and the others ran outside to see what was happening. They looked in the direction of the Everfree Forest to see a line of black figures marching their way towards town. Some were flying but most were on the ground. They quickly realized that the black figures were actually more living dolls.

"There's more of them?!" asked Derpy timidly.

"What the hell's going on?!" snapped Rainbow Dash.

"An invasion," said the Doctor.

"We've got to stop them from reaching the town!" said Twilight as she began running towards the edge of town. The Doctor and the others chased after her.

Some of the pegasus dolls had managed to reach the town earlier than the others. Ponies ran in fear as long arms of hair reached for them. Twilight and Spike used fire to fight off the dolls while the Doctor used his Sonic Screwdriver to disable the arms. Rainbow Dash and Fluttershy took to the sky and fought the dolls in the air, though Rainbow Dash did most of the fighting. They eventually made it to the edge of town and the doll army was approaching fast. Some of the other ponies in town had come together to form a makeshift militia to ward off the dolls. Applejack looked and saw that Big Macintosh was leading them.

"Be careful, Big Mac!" she called.

"Eeyup!" he called back.

"Not much of a talker, that one," said the Doctor.

"So what do we do now?" Derpy asked as they turned to face the dolls.

"We take them down. It shouldn't be too hard. We've managed to take down a few already."

"That doesn't make this look any easier," Twilight gulped. Suddenly, something heavy landed next to the Doctor. It was a large blue cannon with purple wheels, which had pictures of flowers on them.

"I'm ready!" said Pinkie Pie as she aimed her party cannon.

"Where did that come from?!" asked the Doctor.

"I never go anywhere without my party cannon!"

"But how could you carry that? It's as big as you are!"

Twilight patted the Doctor on the shoulder and said, "Doctor, it's best not to try and make sense of what Pinkie does."

"But how did-"

"Please, Doctor. Drop it. Even _your_ head would explode if you tried to find out how Pinkie Pie's mind works."

The Doctor still had plenty of questions but he figured that he'd probably never get a satisfying answer.

Big Mac and his militia were the first to charge. Rainbow Dash flew alongside them.

"Okay, Doctor! You, me, and Applejack will head out with the others!" said Twilight. The unicorn then looked back at the others. "Spike. You, Rarity, Fluttershy, Pinkie Pie, and Derpy will hold back and fend off any dolls that break through." She looked into the dragon's eyes to see that he was still upset. She knelt down to his level and kissed him on the forehead. "I'll be fine. Remember the promise I made five months ago?"

"Yeah," Spike replied.

"I said that I would come back. It may have taken longer than either of us expected but I managed to keep that promise. I'm back now. Please don't be mad anymore, Spike."

"I don't want to be mad anymore, Twilight. But that still doesn't change the fact that you just up and disappeared for nearly half a year."

"Can we discuss this later? We have bigger problems on our hooves at the moment!" said Applejack. The Ponyville militia and the dolls had already begun to clash. The Doctor and Twilight nodded to each other and followed Applejack out into the battlefield. Pinkie stood behind her party cannon and waited.

"He sure is a strange stallion isn't he? The Doctor," said Rarity.

"Strange, but I trust him nonetheless," said Fluttershy.

"I'm not done with my conversation with him yet," said Spike.

"He's going to save us. I know he will," said Derpy.

_**The Edge of Town, Ponyville, Equestria, Gaia, Autumn, 1002 C.E.**_

The fight was having mixed results. Some of the dolls had managed to capture some of the ponies and had taken them back into the Everfree Forest. The Doctor and Twilight were a force to be reckoned with. If one was caught then the other would free them. The Doctor was beginning to like the Sonic Screwdriver's new abilities. At one point he actually managed to make one of the dolls sink into the earth but he was unsure about how he had been able to do it. If there was one thing the dolls hated, it was fire. Twilight found herself relying mostly on fire spells during the fight. The dolls' hair arms didn't stand a chance against the orange flames. Applejack and Rainbow Dash were also making up a good team. Rainbow Dash picked up Applejack and Applejack used her strong hind legs to kick the dolls as she sped through the air. A few dolls managed to get beyond the militia but Pinkie was able to fend them off with her party cannon and Spike sent them running away with his fire blasts. Derpy, Fluttershy, and Rarity teamed up to fight a doll that had three heads for some reason. Fluttershy and Rarity managed to distract the doll while Derpy took it out from behind with a frying pan.

"Good going!" Rarity complemented. The fight must have lasted for around twenty minutes before the dolls began retreating into the forest.

"They're retreating!" Twilight cheered.

"Eeyup!" called Big Mac. Most of the ponies had received only minor injuries from the fight but that still didn't change the fact that some of them had been taken.

"What do they want?" asked Fluttershy as everypony grouped up again.

"Any ideas, _Doctor_?" Spike asked.

"Not really. We just need to find out the identity of their master and then we can find out how to win this battle," the Doctor replied. He turned back towards the forest. "They'll be back soon. I'm guessing we have an hour at max before they decide to strike again."

"How can you be so sure?" Pinkie Pie asked.

"I've seen enough battles in my life to know how battle tactics work."

"So what's the plan now?" Applejack asked.

"We might want to try and establish some form of protection over the town just in case they try to play dirty and strike when we're recovering," Rarity suggested.

"Good thinking, Rarity!" said Twilight. "I think I know just the thing. I learned how to cast this following my brother's wedding."

Twilight's horn began to glow and a large blast of energy shot up into the sky. Within seconds, a massive, purple barrier had formed around Ponyville. Twilight then fell to the ground.

"Are you okay?!" Spike asked.

"I'm fine. It's just a very demanding spell," replied the weakened unicorn. "This should give us a couple hours of protection at max."

"This can give us some time to find out more about our enemy," said Rainbow Dash.

"Right," said the Doctor. "And I think I know just where to start."


	5. Cracks

Chapter 4: Cracks

_**Sugar Cube Corner, Ponyville, Equestria, Gaia, Autumn, 1002 C.E.**_

The Doctor and the others had decided to group up inside Sugar Cube Corner until the force field disappeared. The Doctor was busy examining two of the now deceased living dolls with his Sonic Screwdriver.

"Found anything out yet, Doctor?" asked Twilight.

"Not much. Now they're just rags sewn and stitched together. There's nothing remarkable about them at this point," he replied. "However, I was able to find traces of a very powerful form of magic."

"What kind of magic?"

"Tell me, Twilight. Have you ever used magic to animate inanimate objects?"

"Not really. It's a very tricky spell to pull off and, even then, it can drain a unicorn's energy in a flash."

"Well it's obvious to me that our foe is either a unicorn or an alicorn, a very powerful one at that. All of these dolls are being animated and controlled by one single being. I think it's obvious that our foe has a lot of energy inside them to spare."

"At least we know what species our enemy is now," said Derpy. The Doctor stood up and turned towards his companions.

"Well, are there any other creatures in this world that can use magic aside from unicorns and alicorns?"

"Ah don't think so," Applejack replied.

"There could be but nopony's discovered a creature able to control magic yet," said Rarity.

"Come on! Magic surely isn't just limited to unicorns and alicorns! You earth ponies and pegasi must have some sort of magical abilities within you!" said the Doctor. The ponies looked amongst each other and then turned back to the Doctor.

"We pegasi have some form of magic in us which allows us to fly," said Rainbow Dash.

"I've read that earth ponies are stronger than the other ponies in terms of physical strength and connection to the earth," Twilight informed.

"Duh! Everypony knows that, silly!" Pinkie Pie exclaimed as she wrapped one of her arms around Applejack.

"Interesting but, as of now, I think everything points towards the magical workings of a unicorn or alicorn," said the Doctor. Twilight stumbled for a bit but Spike managed to help her regain her balance.

"You okay?" asked the dragon.

"I'm fine. That protection spell just wore me down a little bit," Twilight replied.

"How long do you think we have until the shield drops?" Fluttershy asked.

"An hour at least."

"Damn!" said the Doctor. He looked down at the dolls and stared straight into their button eyes. "Come on. What secrets are you hiding? I know the answer's here somewhere. It's right on the tip of my tongue and yet I can't spell it out!" He began pacing around the shop and mumbling to himself. "Magic. Control. Animation. Life. Mind. Mind control. Unicorn. Alicorn. Wait a minute. Mind control. Magic. Unicorn. Oh no. Oh no no no! I hope I'm wrong about this!"

"What's wrong, Doctor?"

The Doctor grabbed Twilight and pulled her off to the side.

"Twilight, do you remember when we traveled to 2002?" he asked.

"How could I forget?" she responded.

"Remember what happened while we were there?"

"Like I said, how could I forget?"

"Doesn't all of this sound a little bit familiar to you?"

"Something _has_ been eating at the back of my mind but I can't figure out what."

Then it hit her. She looked at the Doctor and said, "No. Are you suggesting-"

"It's possible."

"But how can _she_ be here? I didn't think that she existed yet."

"I don't think she does but what if she got her hooves on some time traveling technology. It's obvious that your kind are going to gain time traveling devices in the future. I mean, look at Matilda and her _borrowed_ vortex manipulator."

"But how could she have gotten her hooves on one of those?"

"I don't know. But we might find out soon enough."

"How can we even be certain that it's even her behind all of this?"

"There are too many coincidences going on here. The powerful magic. The somewhat-mind control. It's all sounding like the influence she had, or will have, over Celestia in 2002."

"I know I don't say this a lot but I _really_ hope that you're wrong, Doctor. I don't have the strength to put up with her at the moment."

"I with you on that one, Twilight."

"So what are you two talking about?" asked Pinkie. The Doctor and Twilight jumped as they realized that Pinkie was standing right next to them.

"Bloody hell, Pinkie Pie!" the Doctor exclaimed.

"So what _were_ you talking about exactly?" Spike asked.

"The possible identity of our enemy," Twilight replied.

"So who do you think it is?" Derpy asked. The Doctor was about to begin his explanation when a loud crack ripped through the air and the entire town seemed to shake around them. "What was that?!"

"Trouble," said Applejack.

_**Outside Town Hall, Ponyville, Equestria, Gaia, Autumn, 1002 C.E.**_

The sky seemed to turn a burnt orange as large, red cracks appeared in Twilight's magic barrier. Ponies looked towards the sky as the cracks attempted to grow larger than they already were.

"Oh my!" exclaimed Fluttershy as red sparks began falling towards the ground in showers.

"This doesn't look good!" said Rarity. Flying dolls were pounding on the exterior of the shield and an army was stationed around the town. It was much larger than the army they had previously faced.

"Where's a good army when you need one?!" asked Applejack. The ground began to shake violently. Buildings around them shook and some nearly collapsed, though the unicorns and pegasi in town managed to keep the buildings stable. A loud, robotic voice echoed through the air.

"I will destroy this town if it's the last thing I do! But I might be willing to be kinder if two certain someponies decide to make a generous sacrifice," said the voice. The Doctor could tell that this wasn't their enemy's true voice but he also knew all too well who these _two certain someponies_ were. The ground slowly began to stop shaking and the cracks in the field healed themselves.

"What's happening?" Rainbow Dash asked.

"Fail safe," Twilight replied. "I added an extra punch to my protection spell so that the enemy wouldn't have an easy time breaking through the defenses."

"Nice going, egghead! It sure is nice to have ya back!"

"You said it!" said Spike. A smile began to appear on his face but it quickly disappeared. Twilight sighed and looked away. She didn't have the strength to think about her guilt at the moment.

"So who's the pony causing all of this trouble?! You two had an idea about who it was, right?!" asked Pinkie. The Doctor stepped forward and cleared his throat.

"Twilight and I believe that it may be an enemy of ours that we came across during our travels," he said.

"Who is this enemy of yours?" asked Rarity.

"Her name's Thalia," Twilight replied. "She's...uh...it's kind of hard to explain."

"Spit it out already!" Applejack urged.

"She's a clone of me."

"A clone?!" everypony gasped aside from the Doctor and Twilight.

"Yeah. But she hasn't been created yet."

"Hold on! How can a clone of you, who hasn't been created, be attacking us now?" Rainbow Dash asked.

"You met her when you traveled into the future, didn't you? And she's managed to travel back in time." Fluttershy stated. Everypony fell silent.

"What?" Applejack asked. Fluttershy instantly covered her mouth and blushed.

"I'm sorry! I guess Fluttershy's the only pony who I told about this!" said Twilight nervously. "You see, the Doctor's ship doesn't only travel through space. It travels through time as well." Everypony remained silent. "That's why I came back five months late. From my point of view, only a few days have passed since the day I left. The Doctor thought that he had brought me back five minutes later...only to find out that he brought me back five _months_ later."

"It's an honest mistake! The TARDIS can be really unpredictable sometimes and she's still healing from the wounds that blasted Dalek gave her!" said the Doctor.

"You actually traveled through time?" Spike asked.

"Well it's not like I haven't done it in the past," said Twilight.

"But this is different! That was just a spell that took you back a week for only a few seconds. This is actual, full-fledged time travel!"

"What did you see?!" asked Rainbow Dash.

"Where did you go?!" asked Pinkie Pie.

"Why don't we focus on that stuff later?" asked Derpy as she pointed towards the sky. The cracks were beginning to appear again.

"Good idea!" said the Doctor. Suddenly, the ground began shaking underneath them once again. This time it was much more violent.

"Everypony hang onto something!" Twilight cried. Just then, the ground split open and Twilight, Pinkie Pie, and Spike fell into the dark abyss.

"Twilight! Pinkie! Spike!" cried Rarity. Fluttershy gasped.

"I'll get them!" said Rainbow Dash and, with a flash, she flew down into the dark earth. The seconds seemed to tick by like hours as they waited for the return of their friends. The Doctor's hearts were beating out of his chest. Then they saw them quickly flying towards the surface. Pinkie Pie giggled with delight as Rainbow Dash flew her, Twilight, and Spike back above ground. Then, the ground shook again and large, brown vines wrapped around Twilight and Rainbow Dash. "Let go of me!"

Pinkie managed to jump to safety with Rainbow Dash's help and she brought Spike along with her.

"Twilight!" cried Spike.

"Rainbow Dash, grab my hoof!" called the Doctor. The Doctor reached for Rainbow Dash while Spike reached for Twilight. They were about the touch when the vines began to pull on them once again. Derpy and Fluttershy flew in to stop the vines but the vines quickly retaliated and flung the two pegasi into a nearby pond. A series of black figures began emerging from the abyss below. The Doctor realized that it was an entire army of living dolls. Spike and Twilight tried to burn the flames but it was to no avail. The dolls seemed to laugh as Twilight and Rainbow Dash were pulled deeper into the abyss. The Doctor attempted to stun the vines with his Sonic Screwdriver but, again, it was to no avail. "Damn! Something's protecting them!"

"Twilight! Rainbow!" Applejack called.

"No!" cried Spike. Twilight's horn lit up as she looked up towards the surface, which was growing further and further away.

"Don't worry, Spike! I'll come back! I promise! I always keep my promises!" she called. The dolls began to grab onto them along with the vines.

"Twilight Sparkle! Rainbow Dash! You listen to me!" called the Doctor. The trapped ponies looked up at the chestnut stallion. "I will find you no matter what it takes. Whether our enemy's Thalia or not, they made a big mistake when they decided to attack us. I _will_ find you! I _will _save you! This town will _not_ fall as long as there is a Doctor to defend it! Do you hear me?!"

Twilight and Rainbow Dash nodded and smiled sadly as the darkness ate them up. The earth then closed up, leaving the Doctor, Derpy, Spike, Applejack, Pinkie Pie, Fluttershy, and Rarity alone with their fears.

"Did you mean all of that?" Spike asked. The Doctor looked into the dragon's eyes. They were puffy and red with sadness and anger, but mostly sadness. He knelt down to the dragon's level and nodded.

"Every word. I've lost to many companions and friends already. I promise you, Spike. I will not let anything happen to Twilight. I'll bring her back. As long as I'm around. You can always be assured by the fact that, no matter what it takes, I will bring her, Rainbow Dash, or any of your friends home when they are lost and/or put in danger. Do you believe me?" the Doctor replied. Spike wiped away the tears and faced the Doctor with a confident smile.

"I do."

The Doctor and Spike then turned to the sky to see a shower of red sparks raining over the town.


	6. Present for the Doctor

Chapter 5: Present for the Doctor

_**Outside Town Hall, Ponyville, Equestria, Gaia, Autumn, 1002 C.E.**_

"So what do we do now?" Fluttershy asked as red sparks continued to rain down from the sky above.

"The barrier will fall soon and that's when the dolls will strike. This town will not be able to fend off all of them," the Doctor replied glumly.

"But there's hope. Isn't there?" asked Rarity.

"Of course there is. This town will never fall as long as I'm here!"

The town shook again beneath their hooves and the buildings shifted a bit.

"It looks like we don't have much time," Spike croaked.

"Then let's get to work, you silly fillies!" said Pinkie Pie.

"Last time I checked, Spike and I were not fillies," said the Doctor with a grin.

"Okay! Come on, silly fillies, stallion, and dragon!"

"Much better!"

_**Castle of the Regal Sisters, Everfree Forest, Equestria, Gaia, Autumn, 1002 C.E.**_

Twilight slowly regained consciousness. Her head was spinning and her entire body vibrated with pain. Dirt covered her coat and her mane was strewn. She was sitting up with her legs bound together. She turned around to see that she was tied to an unconscious Rainbow Dash, whose legs were also bound. Twilight's vision eventually cleared and she suddenly realized where she was. It was a large, stone room with broken windows, no roof, and vines stretching over the ancient stone walls. The last time she saw this room was when she and her friends had fought Nightmare Moon two years previously.

"Brings back memories, doesn't it?" asked a voice from the darkness. Twilight looked to see a cloaked figure approach her. She was beginning to wonder why villains always wore black cloaks when the hood slowly fell down. Twilight gulped. The villain standing before her was a mare with pitch black eyes and hair, a pale white coat, and blood-red lips. The mare also had an extremely familiar face; it was Twilight's own face.

"Looks like we meet again, Thalia," Twilight groaned. Thalia chuckled as she approached her prisoners. Twilight couldn't help but notice that her clone looked extremely different from how she had looked, or would look, in 2002. Her coat was shinier, her eyes emitted more fearful power, and her lips were redder and vibrant. This Thalia definitely had a long way to go before she became the Thalia that died 1000 years in the future.

"You don't look so happy about it, _Twiley_."

"Maybe it's because I'm not. Ever think about that?"

"Every day."

A greedy smile appeared on Thalia's face. The clone approached Twilight and made direct eye contact with her.

"I've waited so long, dear Twilight," Thalia said. "At least five months."

"You've been in Equestria since June?!" Twilight asked.

"Why of course. You didn't think I was going to sit back and let you destroy me again? You and that Doctor ruined my chances of a new life. A life together with _him_."

"With who?"

Tears were now slowly rolling down Thalia's cheeks.

"You, of course, wouldn't know. I should probably be saying that you're _going_ to ruin my chances with him. No matter. I was able to get my hooves on a very helpful device and now I can finally seek my revenge."

Twilight looked and saw a vortex manipulator wrapped around Thalia's left front hoof.

"So...what are you planning on doing?"

"Killing you and the Doctor and destroying that pitiful town in the process."

There was no surprise there.

"Thank you for disappearing for five months, Twiley," Thalia continued. "I needed that time to prepare my army."

"You mean the dolls?"

"Exactly. I appeared in Ponyville right after you and the Doctor left. I may not have all of your memories but I do remember the time when you left with the Doctor for the first time. I knew when you'd return so I spent my time waiting and preparing so that I would be ready to present you with my welcome home gift!"

"Sadly, I don't really like it. Can I get a refund?"

Thalia punched Twilight in the nose and took a few steps back.

"Don't worry, Twiley. The fun is not yet over. I still have one last present for the Doctor. Once I have both you and him in my clutches then I'll just let the dolls go ahead and destroy the town. I just hope _she_ doesn't interfere again."

Twilight wanted the ask about this _she_ but was more concerned about another topic. She looked at Thalia and asked, "What about the ponies that your dolls took?"

"I haven't killed them yet. I think I'll have some fun with them first. Things are going to work out differently this time. He'll be all mine and I'll be the one with the happy ending!"

"Listen, Thalia. Messing with time is not the answer here!"

"Oh shut up! Nopony tells me what to do! Not you! Not the Doctor! Not anypony! Well maybe _him_ but he's the exception!"

"Who the hell is this _him_ that you keeping talking about?!"

"You'll never live to find out. I'm going to let you die with that secret slowly burrowing away at your subconscious."

"Subtle."

"Oh shut up already! Now, if you'll excuse me, I've got a message to send to the Doctor."

Thalia turned around and walked out through the rotting, wooden doors. Twilight heard a groan behind her as Rainbow Dash slowly woke up.

"What happened?" she groaned. The pegasus then realized that she was tied up and began fighting the bonds with all of her strength. "Damn! These knots are tight!"

"It's no use, Rainbow Dash," Twilight groaned.

"Twilight! Could you try and untie these ropes?"

"I can't. My magic has no effect on them. Thalia must have put an enchantment on them or something of that nature."

"Thalia? That clone of yours that you mentioned? So she _is_ behind all of this?!"

"Yes. It's a long story, and there are parts of it that I don't really understand, but Thalia's the culprit behind this invasion and now she's going after the Doctor."

"What's going to happen to us and the town if she wins?"

"We'll die eventually and the town will be destroyed."

"Oh. No pressure then, huh?"

"No. No pressure at all."

Twilight gulped as she felt the ropes grow somewhat tighter.

_**Home of Twilight Sparkle, Ponyville, Equestria, Gaia, Autumn, 1002 C.E.**_

The Doctor burst through the doors of the library in a flash. Derpy, Spike, and the others followed close behind him.

"What are you planning, Doctor?" Derpy asked.

"A rescue mission. Plain and simple!" the Doctor replied. He rushed over to the TARDIS and tried opening the doors.

"Would you care to go into greater detail about this here _rescue mission_ of yours?" Applejack asked. The Doctor turned around to respond but then fell silent.

"Wait a minute."

The Doctor began banging on the TARDIS doors and even clapping loudly several times. He inserted a key into the slot but nothing worked. The doors were shut tight.

"What's wrong, Doctor?" Pinkie Pie asked as she stopped jumping with nervous excitement.

"The TARDIS doors are shut tight."

"And that means what exactly?" Rarity asked.

"This was my rescue mission in a nutshell. I'd find Twilight with help from the TARDIS, bring her back into the town, and we'd work out what to do from there with your help. But, for some reason, the TARDIS won't open!"

"Does it do that often?" Derpy asked.

"No! Well, there was this one time where I think I insulted it and it was being stubborn about the whole thing...or maybe that was because the doors hadn't been greased in over a century at the time."

"How can a box be stubborn?" Spike asked.

"Oh you'd be surprised. This _box_ has had more stubborn moments than a mule!"

"I know a few mules and they can be pretty stubborn," said Pinkie Pie.

"My point exactly!"

"So what's the plan now?" Fluttershy asked.

"Plan B of course!"

"And what's plan B?" Spike asked.

"I have no flipping idea, but I'll come up with something soon!"

The ground shook violently again and screams from ponies emanated from outside.

"Hopefully incredibly soon!" the Doctor continued with a forced smile. The library shook around them and, suddenly, a holographic image appeared in the center of the room. At first, everypony thought it was Twilight. But, when they looked closer, they realized that though it looked like Twilight, the mare before them was not their beloved friend.

"How nice to see you all again! I believe the last time we met you were destroying my life! Now I get to destroy _your_ lives? Isn't that great?!" asked the Twilight clone with a happy-go-lucky tone.

"Thalia!"

"Doctor! How nice to see you again! Tell me! Are you enjoying your locked TARDIS?"

"How did-"

"Just a little trick of mine. That TARDIS isn't opening again for quite a while."

"What do you want, Thalia?"

"Justice, Doctor."

"There's a big difference between justice and revenge."

"Well, in my case, they're one in the same. Don't worry about Twiley and Dashie. I'm keeping them nice and tied up for future use."

"LET THEM GO!" Spike snapped. Thalia turned to Spike and laughed.

"I remember you! Spike. The dragon Twilight left behind."

"SHUT UP!"

"I have some of Twilight's memories, Spike. I remember what Twilight was thinking on the day she left to _help_ the Doctor. She was thinking about how boring how life was in Ponyville. How much she longed for a better life. How she longed to get away from her stupid friends. That hillbilly, Applejack, that pansy, Fluttershy, that brat, Rarity, that idiot, Pinkie Pie, that jerk, Rainbow Dash, and that weak, stupid, crybaby dragon, Spike. She was glad to get away from you."

"SHUT UP!"

"You know it's true, Spike. Why else would Twilight leave to help out a stallion that she had only recently met. Face it. You're nothing in her eyes. You were always nothing, you are nothing to her now, and you'll always be nothing. Always coming second to the Doctor."

Spike blew a blast of fire at Thalia but it did nothing due to her being a hologram.

"Leave this town in peace, Thalia. If you don't then I will have to stop you," the Doctor warned.

"Come and get me, Doctor! Oh wait! You won't _have_ to come to me because I've already established your transportation."

"What's that supposed to mean?"

"I have one, final present for you, Doctor. I hope you enjoy it."

Thalia cackled as her holographic image disappeared.

"I didn't like the sound of that," said Derpy. Suddenly the ground shook again, but this time it was different. The shaking wasn't coming from something below ground but rather was coming from something above ground. Ponies outside began screaming and the lights in the library went out, leaving the ponies and the dragon in almost complete darkness. "I _really_ don't like the sound of that!"

The shaking stopped and everything fell silent. That's when the roof caved in.


	7. A Big Predicament

Chapter 6: A Big Predicament

_**Home of Twilight Sparkle, Ponyville, Equestria, Gaia, Autumn, 1002 C.E.**_

Derpy grunted a bit as the Doctor jumped on top of her and Spike, shielding them from the debris. Rarity produced a small, protective barrier at the last second to protect herself and Fluttershy. Applejack and Pinkie Pie ducked under Twilight's coffee table. Thankfully, only a medium-sized portion of the roof fell in but it was large enough to cover Applejack and Pinkie Pie entirely and cover the Doctor, Derpy, and Spike in a few inches of dust. The Doctor looked up to see the massive face of a living doll looking down at him. The doll was at least the same size, if not larger, than the library itself. It's mouth was open and was big enough to grab six ponies at once. Its razor teeth were the size of chairs and were sharper than kitchen knives. Its tongue was long and it drooped out of the mouth like a soggy rope.

"Get out! Everypony get out now!" ordered the Doctor. Rarity and Fluttershy quickly made their way through the door. The Doctor rushed over to a pile of debris to free Applejack and Pinkie Pie. The doll opened its mouth and bared its teeth at the Doctor. The Doctor has just grabbed a hold of one of Applejack's legs when he noticed the teeth of the doll were mere feet away. "Well this _certainly_ isn't going to end well."

Suddenly, a gray blur flew past the Doctor and smashed into the doll's face. Derpy flew up towards the ceiling and dive bombed the doll again.

"You leave the Doctor and the others alone you giant rag!" she snapped as she proceeded to kick one of the doll's button eyes. She looked down at the Doctor, who seemed to be frozen with a mix of surprise and amazement. "What are you gawking at! Get out of here while I distract it!"

The Doctor returned to his senses and helped the two earth ponies out of the wreckage. Spike blew a large blast of fire at the doll before following Fluttershy and Rarity through the doorway. The Doctor, Applejack, and Pinkie Pie ran through the doorway while Derpy flew out through the hole in the ceiling. The giant doll let out a shrill cry and began its pursuit of the Doctor.

"How the hay did that thing get beyond the barrier?!" asked Applejack. The Doctor looked to see a large hole located near the library.

"My guess is that Thalia hid a secret doll army underground, just in case a protective barrier was set up," the Doctor replied. Normal-sized dolls were now climbing out of the hole and were proceeding to attack nearby ponies. The barrier was riddled with cracks and the Doctor could only assume that the town had a few minutes left before the barrier finally gave away. Spike, Fluttershy, and Rarity ran into a nearby home and waved at the Doctor, Derpy, Applejack, and Pinkie Pie.

"Get in here! Quickly!" Fluttershy hissed. The Doctor ran into the house and was followed by the others. Fortunately, the large doll hadn't seen the Doctor disappear into the house and had lost sight of him.

"It looks like we've lost it," said Derpy.

"For now!" Pinkie Pie said with a shiver.

"Come on, Pinkie Pie. Try to think more optimistically!" said Rarity.

"You mean like think about how at least we're going to die quickly?" asked Spike.

"Not really what I was going for."

"Whose house are we in, anyway?" the Doctor asked.

"I'm not sure at the moment. Though ah think they wouldn't mind us hiding in here for a bit," Applejack replied.

"I hope Angel Bunny and the others are alright," said Fluttershy.

"Who?" the Doctor asked.

"My animal friends."

"Fluttershy has a huge amount of animals living at her house. It's almost like going to a zoo!" Pinkie Pie exclaimed. The Doctor chuckled and turned to Fluttershy.

"So you have a magical touch when it comes to animals?" he asked.

"I guess so," replied the shy pegasus.

"So I guess you're like the pony version of Snow White."

"Who's Snow White?"

"I'll tell you later."

Suddenly, the Doctor felt a sharp pain ring throughout his head. He crumpled to the ground and grabbed his skull in pain.

"Oh my Celestia! I'm so sorry!" said a soothing voice. The Doctor looked to see a cream-colored mare and a green mare standing a few feet away from him and the others. The cream-colored mare was holding a frying pan.

"Now I remember! We're in Lyra and Bon-Bon's place!" said Pinkie. Derpy knelt down next to the Doctor and examined the whelp on his head.

"What was that for, Bon-Bon?!" Derpy snapped at the cream-colored mare.

"I'm sorry! I thought he was another one of those dolls!" Bon-Bon exclaimed.

"Well, as you can see, I'm not. I'm just a stallion...with internal bleeding in his cranium," said the Doctor as he stood up with Derpy's help.

"What the hell's going on out there?!" Lyra snapped.

"A party. What do you _think_ is happening?!" Spike asked with a snarky tone.

"I don't think this is a party, Spike," said Pinkie Pie. Spike simply face-clawed and gave an audible _ugh_.

"Everything's going to turn out alright, right?" Bon-Bon asked. "These creatures are going to go away, right?"

"They won't destroy this town. I promise you," said the Doctor. That's when the ground began shaking underneath their hooves.

"It's coming back!" gasped Fluttershy.

"What's coming back?" Lyra asked.

"Do you have a cellar?" asked the Doctor.

"Yes."

"I suggest hiding down there for a little bit."

Lyra was about to ask another question but Bon-Bon quickly grabbed her and pulled her through a nearby door. The door was shut quickly and locked soon afterwards.

"We better go. I don't think any of us wants to be responsible for another destroyed home," said Derpy. Everypony agreed and quickly ran out through the front door.

_**Outside Sugar Cube Corner, Ponyville, Equestria, Gaia, Autumn, 1002 C.E.**_

The giant doll continued its pursuit of the Doctor and the others. Spike had spewed fire at it, Derpy had kicked it, Applejack had tried taking out its legs, the Doctor had used his Sonic Screwdriver, Pinkie had shot it with her surprisingly-portable party cannon, Fluttershy had attempted to convince it to go away, and Rarity had tried using one of Twilight's fire spells. Nothing seemed to work on it.

"We've got one tough customer with us today!" said Pinkie as she fired the cannon again, covering another part of the doll in multicolored streamers. Derpy tried kicking it again but ended up getting caught in an arm of living hair. Derpy thrashed as the arm pulled her closer towards the doll's open mouth. Suddenly, a little blur flew out of an upper window of Sugar Cube Corner and began zipping around the doll's face. It took the ponies down below a few seconds to recognize the blur as Pound Cake. "Get out of there!"

Mr. and Mrs. Cake were standing by the open window with Pumpkin Cake. Their faces were whiter than flour. Pound Cake was able to distract the doll, which allowed Derpy to break free. Pound Cake flew back into his parents' arms but now the doll had turned its attention on the store.

"Oh no!" exclaimed Applejack as the doll swatted one of its hooves at the shop. The shop shook on its foundations and parts of the upper floor began caving in. Derpy and even Fluttershy flew up to try and draw the doll away from the store but nothing worked.

"Mr. Cake! Mrs. Cake! Get out of there!" Pinkie cried. The doll smiled gleefully as the shop began leaning dangerously. The Cakes tried to make it downstairs but the floor began to fall apart underneath them. Spike tried blasting more fire at the doll but, as always, it did no good. Spike then turned to say something to the Doctor, only to see that the chestnut stallion had disappeared.

"Where did the Doctor go?" Spike asked.

"Wasn't he standing right there a moment ago?" Rarity asked.

"Where could he have gone off to?" Applejack asked. Suddenly, a series of yells began emanating from upstairs. It was the Doctor.

"Hey! Big, tall, and messy!" the Doctor called as he stepped towards the upstairs window that was closest to the doll's face. "Thalia sent you to get me, right? Well take me then! Leave these ponies alone!" The Doctor turned back towards the Cakes and beckoned them towards the stairs. The Cakes quickly, but quietly, made it out of the shop. "I'm right here! Go ahead and take me!"

The Doctor pulled out his Sonic Screwdriver and aimed it at the doll's face.

"What are you doing?!" cried Derpy from the ground.

"Improvising!" the Doctor replied. The doll's mouth opened and its large tongue fell out. The Doctor was about to activate the Screwdriver but the doll's tongue reacted at speeds the Doctor couldn't even fathom. It wrapped around the Doctor, crushing all of the air out of his lungs, and pulled him into the doll's mouth. Derpy watched in horror as the Screwdriver fell towards the ground and landed at her feet. The giant doll smiled joyfully and began sinking into the ground.

"NO!" Derpy cried as she flew up towards the doll's face. The doll swatted Derpy like a fly and sent her falling towards the ground. Applejack managed to catch her.

"Gotcha!" she said. The doll disappeared into the earth, leaving nothing behind but a small sinkhole. Derpy punched the ground with her hooves.

"He can't be gone! This _can't_ be over with!"

"Don't look now but I think we have company!" said Pinkie. A horde of dolls was now starting to surround them. Twilight's protective barrier was finally starting to break apart for the last time.

"We can't take them all on!" said Rarity.

"We have to fight! We have to save Twilight, Rainbow, and the Doctor!" said Applejack.

"We _have_ to save them!" Spike said. The dolls were ganging up on them now. Their hair was extending and their sharp teeth was gleaming. Suddenly, there was a massive, red burst of energy that seemed to envelope the entire town. The crumbling barrier healed itself and all of the dolls crumpled to the ground like rags. They were lifeless. "Wait. What in the name of Celestia just happened?!"

"Improvising," replied a familiar yet unfamiliar voice. The mares and the dragon turned to see a dark blue stallion approaching them. He was a unicorn with a silver mane, sharp, indigo eyes, a fine, black suit with a red tie, and an hourglass cutie mark. In his mouth there was a cylindrical metal device with a red tip. The stallion stashed the device away into one of his suit pockets.

"Are you the one who saved us?" Fluttershy asked.

"That is correct, dear Fluttershy. I just used my Sonic Screwdriver to get rid of those annoying dolls. God, they annoyed me back then and they still annoy me now."

"What?" Spike asked.

"Nothing. Just talking to myself. Anyway, fear no longer. I'm here to fix everything! This town is not going to fall, your friends are going to be saved, and I'm going to use all of my strength and knowledge to help you out of this _little_ jam!"

"I just have one question," said Derpy. "Well two, actually."

"Ask away, dear Derpy Hooves!"

"How do you know us and who exactly are you?"

"I believe I can answer those two questions with one simple answer."

"And that answer is?"

"I'm the Doctor."

To be continued...


End file.
